Contacts of the strand formed by residues 288 - 295 (chain A) in PDB entry 1SDW


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with ILE 288 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226A  SER*     4.2     4.9    -      -       -      -
    227A  CYS      3.3    12.6    -      -       -      +
    228A  GLN*     4.2    22.2    -      -       +      +
    254A  ARG*     3.6     2.6    -      -       -      -
    255A  VAL*     2.7    44.3    +      -       +      +
    286A  GLY      4.4     3.1    -      -       -      +
    287A  ASP*     1.3    79.0    -      -       -      +
    289A  LEU*     1.3    73.9    +      -       -      +
    290A  ALA*     4.8     0.2    -      -       +      -
    338A  VAL*     5.1     5.2    -      -       +      -
    339A  ALA*     4.6    11.7    -      -       +      -
    342A  MET*     3.6    38.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 289 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205A  TYR*     3.4    50.0    -      -       +      +
    207A  MET*     3.5    15.6    -      -       +      +
    226A  SER*     3.1    25.8    -      -       -      -
    227A  CYS      2.9    14.9    +      -       -      +
    229A  TYR*     4.3     8.5    -      -       +      -
    234A  MET*     3.9    13.2    -      -       +      -
    253A  TYR      3.4     3.1    -      -       -      +
    254A  ARG*     4.4     3.6    -      -       -      -
    263A  ILE*     3.6    31.4    -      -       +      -
    283A  VAL*     3.9    26.0    -      -       +      -
    287A  ASP      4.2     0.2    -      -       -      -
    288A  ILE*     1.3    72.9    -      -       -      +
    290A  ALA*     1.3    59.4    +      -       -      +
    319A  ILE*     4.4     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 290 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207A  MET*     3.9     1.7    -      -       -      +
    225A  ILE      3.3     4.5    -      -       -      -
    252A  GLY*     3.3     1.4    -      -       -      -
    253A  TYR*     2.6    42.6    +      -       -      +
    255A  VAL*     4.2     7.2    -      -       +      -
    260A  TRP*     3.7    26.9    -      -       +      -
    288A  ILE      3.9     0.2    +      -       -      -
    289A  LEU*     1.3    77.3    -      -       -      +
    291A  ALA*     1.3    60.8    +      -       -      +
    342A  MET*     4.0    15.5    -      -       +      -
    343A  PHE*     3.8    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 291 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207A  MET*     3.7    26.9    -      -       +      +
    223A  ALA      3.8     0.7    -      -       -      +
    224A  ASP*     3.4     2.8    -      -       -      -
    225A  ILE*     2.8    44.5    +      -       +      +
    250A  VAL*     5.8     1.6    -      -       +      -
    251A  SER      3.1    12.6    -      -       -      +
    253A  TYR*     5.5     0.9    -      -       -      -
    290A  ALA*     1.3    75.8    -      -       -      +
    292A  ARG*     1.3    63.1    +      -       -      +
    293A  CYS*     6.4     0.2    -      -       -      -
    315A  CYS*     6.1     0.9    -      -       -      -
    317A  LEU*     4.0    15.3    -      -       +      -
    343A  PHE*     3.6     4.5    -      -       -      -
    346A  ILE*     5.5     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 292 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222A  ASN*     3.6    28.0    +      -       -      +
    223A  ALA      3.2     4.7    -      -       -      -
    224A  ASP*     2.8    39.6    +      -       -      +
    249A  VAL      3.9     1.0    -      -       -      +
    250A  VAL*     3.4     3.1    -      -       -      +
    251A  SER*     2.9    33.6    +      -       -      +
    291A  ALA*     1.3    75.0    -      -       -      +
    293A  CYS*     1.3    75.4    +      -       -      +
    294A  VAL*     4.0     4.8    -      -       +      +
    315A  CYS*     4.9     0.2    -      -       -      -
    343A  PHE*     3.8    18.6    +      -       +      +
    346A  ILE*     3.8    35.3    -      -       +      +
    350A  ALA*     4.1    11.3    -      -       +      +
    351A  ASN*     2.7    44.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 293 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221A  VAL      3.8     0.9    -      -       -      +
    222A  ASN*     3.5     3.6    -      -       -      -
    223A  ALA*     2.8    31.5    +      -       +      +
    243A  THR*     4.3     2.5    -      -       +      -
    249A  VAL      3.4     6.1    -      -       -      +
    250A  VAL*     3.7    31.6    -      -       +      -
    291A  ALA*     6.4     0.7    -      -       -      -
    292A  ARG*     1.3    75.4    -      -       -      +
    294A  VAL*     1.3    62.5    +      -       -      +
    295A  PHE*     3.7    19.5    +      -       +      -
    315A  CYS*     2.0    54.5    -      -       -      -
    316A  ASN      4.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 294 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220A  VAL*     4.0    18.6    -      -       +      -
    221A  VAL      3.7     2.2    -      -       -      -
    222A  ASN*     3.7    22.7    -      -       -      +
    247A  GLY*     3.8     2.1    -      -       -      -
    248A  LYS*     2.8    38.1    +      -       +      +
    249A  VAL*     2.8    39.1    +      -       +      +
    292A  ARG*     4.0     7.0    -      -       +      -
    293A  CYS*     1.3    76.0    -      -       -      +
    295A  PHE*     1.3    64.2    +      -       -      +
    350A  ALA      3.3    15.5    -      -       -      +
    351A  ASN*     4.3    12.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 295 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212A  THR*     4.4    10.1    -      -       +      -
    214A  ILE*     3.5    33.7    -      -       +      -
    219A  LYS      3.9     0.3    -      -       -      +
    220A  VAL*     3.5     5.7    -      -       -      +
    221A  VAL*     2.8    40.9    +      -       +      +
    223A  ALA*     3.7    18.6    -      -       +      -
    243A  THR*     4.1     9.6    -      -       +      -
    246A  LEU      3.4     8.7    -      -       -      +
    247A  GLY*     3.8    17.7    -      -       -      -
    248A  LYS*     4.8     2.2    -      -       -      -
    293A  CYS*     3.7    24.0    -      -       +      -
    294A  VAL*     1.3    78.6    -      -       -      +
    296A  THR*     1.3    61.8    +      -       -      +
    306A  ILE*     5.5     1.3    -      -       +      -
    313A  GLU*     3.2    31.6    -      -       +      -
    314A  MET      3.5    19.7    -      -       -      -
    315A  CYS*     3.8    11.4    -      -       +      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il